def _test_rate(self, i, j):
reducer = TwoStateRates(self.rates, [i], [j])
reducer.compute_rates()
rAB = reducer.get_rate_AB()
self.assertAlmostEqual(rAB, self.final_rate, 7)
reducer.compute_committors()
rAB_ss = reducer.get_rate_AB_SS()
print "kSS", rAB_ss
self.assertAlmostEqual(rAB_ss, 1.5, 7)
def run(directory, T, A, B, out_prefix, tstart, reverse=False):
if not reverse:
source = "A"
destination = "B"
direction = "A->B"
else:
source = "B"
destination = "A"
direction = "B->A"
rate_constants, Peq, knorm = make_rates(directory, T)
if True:
fname = "{}.rate_consts".format(out_prefix)
print "saving rate constants to:", fname
with open(fname, "w") as fout:
fout.write("#starting_minimum ending_minimum rate_constant\n")
for (u,v), k in sorted(rate_constants.iteritems()):
fout.write("{} {} {}\n".format(u, v, k/knorm))
print "checking and reducing the graph structure"
try:
rate_constants = reduce_rates(rate_constants, B, A=A)
except Exception:
analyze_graph_error(rate_constants, A, B)
raise
print "computing mean first passage times"
calculator = TwoStateRates(rate_constants, A, B, weights=Peq, check_rates=False)
calculator.compute_rates(use_umfpack=True)
print "computing rates"
kAB = calculator.get_rate_AB()
print "k({}) {}".format(direction, kAB / knorm)
if True:
fname = "{}.rates".format(out_prefix)
print "saving rates and mean first passage times for all minima to reach {} to file {}".format(destination, fname)
mfpt = sorted([(m, t) for m, t in
calculator.mfpt_computer.mfpt_dict.iteritems()])
with open(fname, "w") as fout:
fout.write("#Rates and mean first passage times for each node to reach {}\n".format(destination))
fout.write("#The rate is just the inverse of the mean first passage time\n")
fout.write("#minimum_index rate mean_first_passage_time\n")
for i, t in mfpt:
mt = t * knorm
fout.write("{index} {rate} {mfpt}\n".format(index=i, rate=1./mt,
mfpt=mt))
print "computing committor probabilities"
sys.stdout.flush()
calculator.compute_committors()
print "computing steady state rate"
kSS = calculator.get_rate_AB_SS() / knorm
print "kSS({}) {}".format(direction, kSS)
# print the committors
# get the alternate definition of committors for the nodes in A and B
Acomm = calculator.get_alternate_committors(A, B)
Bcomm = calculator.get_alternate_committors(B, A)
all_committors = calculator.committor_computer.committor_dict.copy()
all_committors.update(Acomm)
all_committors.update(Bcomm)
fname = "{}.committors".format(out_prefix)
print "saving committor probabilities for all minima to file", fname
coms = sorted([(m, c) for m, c in all_committors.iteritems()])
with open(fname, "w") as fout:
fout.write("#probability a trajectory starting from each node ends up "
"in {B} before returning to {A}\n".format(B=destination, A=source))
fout.write("#minimum_index committor_probability\n")
for i, c in coms:
fout.write("{} {}\n".format(i, c))
time_solve = calculator.mfpt_computer.time_solve + calculator.committor_computer.time_solve
print "time spent solving linear equations", time_solve, "seconds"
print "total time", time.clock() - tstart